As the title says, my rt28000usb cards are no longer injecting with the newer versions of BackBox using kernel 4.x. If I downgrade back to 3.19 it appears to work again. I have somewhat found a soultion but I have no idea how to go about implimenting it as I don't know anything about patching:

Reboot, check if you have new kernel with uname -r, and try injection again. If this don't help, we can check other solution. This is easy fix if it's working, because your can remove this packages with apt remove.

However it caused another problem. Because I was using VirtualBox, it would no longer allow me to install Guest Additions after upgrading the kernel to 4.5, throwing out errors but the main one being "-fstack-protector-strong". After much Googling I discovered this was because of the GCC version. I updated this to 5 and was able to install Guest Additions

But for Virtualbox i think that you did to much of work. I had almost the same situation and i just reinstalled dkms. Something like apt-get install --reinstall virtualbox-dkms, but maybe this is new issue i'm not aware. Anyway all back to normal